CCR5_CellScreen

CCR5_CellScreen

CCR5_CellScreen_1 - Pre-processing

Sample annotation

	1	2	3	4	5	6	7	8	9	10	11	12
A		MDAMB468 - WT - 1 - Fixed+Tween - NT.fcs MDAMB468 WT Fixed+Tween 1 NT	MCF7 - WT - 1 - Fixed+Tween - NT.fcs MCF7 WT Fixed+Tween 1 NT	SW480 - WT - 1 - Fixed+Tween - NT.fcs SW480 WT Fixed+Tween 1 NT	SW620 - WT - 1 - Fixed+Tween - NT.fcs SW620 WT Fixed+Tween 1 NT	HCT116 - WT - 1 - Fixed+Tween - NT.fcs HCT116 WT Fixed+Tween 1 NT	HT29 - WT - 1 - Fixed+Tween - NT.fcs HT29 WT Fixed+Tween 1 NT	A549 - WT - 1 - Fixed+Tween - NT.fcs A549 WT Fixed+Tween 1 NT	H1975 - WT - 1 - Fixed+Tween - NT.fcs H1975 WT Fixed+Tween 1 NT	TCV2 - WT - 1 - Fixed+Tween - NT.fcs TCV2 WT Fixed+Tween 1 NT		H2052-484 - WT - 1 - Fixed+Tween - NT.fcs H2052-484 WT Fixed+Tween 1 NT
B		MDAMB468 - WT - 2 - Fixed+Tween - NT.fcs MDAMB468 WT Fixed+Tween 2 NT	MCF7 - WT - 2 - Fixed+Tween - NT.fcs MCF7 WT Fixed+Tween 2 NT	SW480 - WT - 2 - Fixed+Tween - NT.fcs SW480 WT Fixed+Tween 2 NT	SW620 - WT - 2 - Fixed+Tween - NT.fcs SW620 WT Fixed+Tween 2 NT	HCT116 - WT - 2 - Fixed+Tween - NT.fcs HCT116 WT Fixed+Tween 2 NT	HT29 - WT - 2 - Fixed+Tween - NT.fcs HT29 WT Fixed+Tween 2 NT	A549 - WT - 2 - Fixed+Tween - NT.fcs A549 WT Fixed+Tween 2 NT	H1975 - WT - 2 - Fixed+Tween - NT.fcs H1975 WT Fixed+Tween 2 NT	TCV2 - WT - 2 - Fixed+Tween - NT.fcs TCV2 WT Fixed+Tween 2 NT	H226 - WT - 2 - Fixed+Tween - NT.fcs H226 WT Fixed+Tween 2 NT	H2052-484 - WT - 2 - Fixed+Tween - NT.fcs H2052-484 WT Fixed+Tween 2 NT
C		MDAMB468 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs MDAMB468 WT Fixed+Tween 1 aCCR5-Hek/1/85a		SW480 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs SW480 WT Fixed+Tween 1 aCCR5-Hek/1/85a	SW620 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs SW620 WT Fixed+Tween 1 aCCR5-Hek/1/85a	HCT116 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs HCT116 WT Fixed+Tween 1 aCCR5-Hek/1/85a	HT29 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs HT29 WT Fixed+Tween 1 aCCR5-Hek/1/85a	A549 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs A549 WT Fixed+Tween 1 aCCR5-Hek/1/85a	H1975 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs H1975 WT Fixed+Tween 1 aCCR5-Hek/1/85a	TCV2 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs TCV2 WT Fixed+Tween 1 aCCR5-Hek/1/85a	H226 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs H226 WT Fixed+Tween 1 aCCR5-Hek/1/85a	H2052-484 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs H2052-484 WT Fixed+Tween 1 aCCR5-Hek/1/85a
D		MDAMB468 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs MDAMB468 WT Fixed+Tween 2 aCCR5-Hek/1/85a	MCF7 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs MCF7 WT Fixed+Tween 2 aCCR5-Hek/1/85a	SW480 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs SW480 WT Fixed+Tween 2 aCCR5-Hek/1/85a	SW620 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs SW620 WT Fixed+Tween 2 aCCR5-Hek/1/85a	HCT116 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs HCT116 WT Fixed+Tween 2 aCCR5-Hek/1/85a	HT29 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs HT29 WT Fixed+Tween 2 aCCR5-Hek/1/85a	A549 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs A549 WT Fixed+Tween 2 aCCR5-Hek/1/85a	H1975 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs H1975 WT Fixed+Tween 2 aCCR5-Hek/1/85a	TCV2 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs TCV2 WT Fixed+Tween 2 aCCR5-Hek/1/85a	H226 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs H226 WT Fixed+Tween 2 aCCR5-Hek/1/85a	H2052-484 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs H2052-484 WT Fixed+Tween 2 aCCR5-Hek/1/85a
E		H28 - WT - 1 - Fixed+Tween - NT.fcs H28 WT Fixed+Tween 1 NT	ZL34 - WT - 1 - Fixed+Tween - NT.fcs ZL34 WT Fixed+Tween 1 NT	ONE58 - WT - 1 - Fixed+Tween - NT.fcs ONE58 WT Fixed+Tween 1 NT	211H - WT - 1 - Fixed+Tween - NT.fcs 211H WT Fixed+Tween 1 NT	PC3 - WT - 1 - Fixed+Tween - NT.fcs PC3 WT Fixed+Tween 1 NT	LNCAP - WT - 1 - Fixed+Tween - NT.fcs LNCAP WT Fixed+Tween 1 NT	DU145 - WT - 1 - Fixed+Tween - NT.fcs DU145 WT Fixed+Tween 1 NT	A431 - WT - 1 - Fixed+Tween - NT.fcs A431 WT Fixed+Tween 1 NT	LUCA-1 - WT - 1 - Fixed+Tween - NT.fcs LUCA-1 WT Fixed+Tween 1 NT	LUCA-62 - WT - 1 - Fixed+Tween - NT.fcs LUCA-62 WT Fixed+Tween 1 NT	U87 - WT - 1 - Fixed+Tween - NT.fcs U87 WT Fixed+Tween 1 NT
F		H28 - WT - 2 - Fixed+Tween - NT.fcs H28 WT Fixed+Tween 2 NT		ONE58 - WT - 2 - Fixed+Tween - NT.fcs ONE58 WT Fixed+Tween 2 NT	211H - WT - 2 - Fixed+Tween - NT.fcs 211H WT Fixed+Tween 2 NT	PC3 - WT - 2 - Fixed+Tween - NT.fcs PC3 WT Fixed+Tween 2 NT	LNCAP - WT - 2 - Fixed+Tween - NT.fcs LNCAP WT Fixed+Tween 2 NT	DU145 - WT - 2 - Fixed+Tween - NT.fcs DU145 WT Fixed+Tween 2 NT		LUCA-1 - WT - 2 - Fixed+Tween - NT.fcs LUCA-1 WT Fixed+Tween 2 NT	LUCA-62 - WT - 2 - Fixed+Tween - NT.fcs LUCA-62 WT Fixed+Tween 2 NT	U87 - WT - 2 - Fixed+Tween - NT.fcs U87 WT Fixed+Tween 2 NT
G	H2452 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs H2452 WT Fixed+Tween 1 aCCR5-Hek/1/85a	H28 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs H28 WT Fixed+Tween 1 aCCR5-Hek/1/85a	ZL34 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs ZL34 WT Fixed+Tween 1 aCCR5-Hek/1/85a	ONE58 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs ONE58 WT Fixed+Tween 1 aCCR5-Hek/1/85a	211H - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs 211H WT Fixed+Tween 1 aCCR5-Hek/1/85a	PC3 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs PC3 WT Fixed+Tween 1 aCCR5-Hek/1/85a	LNCAP - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs LNCAP WT Fixed+Tween 1 aCCR5-Hek/1/85a	DU145 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs DU145 WT Fixed+Tween 1 aCCR5-Hek/1/85a	A431 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs A431 WT Fixed+Tween 1 aCCR5-Hek/1/85a	LUCA-1 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs LUCA-1 WT Fixed+Tween 1 aCCR5-Hek/1/85a	LUCA-62 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs LUCA-62 WT Fixed+Tween 1 aCCR5-Hek/1/85a	U87 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs U87 WT Fixed+Tween 1 aCCR5-Hek/1/85a
H		H28 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs H28 WT Fixed+Tween 2 aCCR5-Hek/1/85a	ZL34 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs ZL34 WT Fixed+Tween 2 aCCR5-Hek/1/85a	ONE58 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs ONE58 WT Fixed+Tween 2 aCCR5-Hek/1/85a	211H - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs 211H WT Fixed+Tween 2 aCCR5-Hek/1/85a	PC3 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs PC3 WT Fixed+Tween 2 aCCR5-Hek/1/85a	LNCAP - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs LNCAP WT Fixed+Tween 2 aCCR5-Hek/1/85a	DU145 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs DU145 WT Fixed+Tween 2 aCCR5-Hek/1/85a	A431 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs A431 WT Fixed+Tween 2 aCCR5-Hek/1/85a	LUCA-1 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs LUCA-1 WT Fixed+Tween 2 aCCR5-Hek/1/85a	LUCA-62 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs LUCA-62 WT Fixed+Tween 2 aCCR5-Hek/1/85a	U87 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs U87 WT Fixed+Tween 2 aCCR5-Hek/1/85a

Data cleaning

Raw data

Raw data, FSC-A vs SSC-A

Outlier cleaning

Outlier cleaning, FSC-A vs SSC-A

Main cell population gating

FSC-A vs SSC-A, Main cell population gating

FSC-A vs SSC-A, Main cell population gated

Singlets cleaning, SSC

SSC-A vs SSC-H, SSC singlet gating

SSC-A vs SSC-H, SSC singlets gated

FSC-A vs SSC-A, SSC singlets gated

Singlets cleaning, FSC

FSC-A vs SSC-A, FSC singlet gating

FSC-A vs FSC-H, FSC singlet gating

FSC-A vs SSC-A, FSC singlet gated

Cleaned dataset

Cleaned dataset, FSC-A vs SSC-A

Cleaned dataset, Missing samples removed, FSC-A vs SSC-A

CCR5_CellScreen_2 - Pre-processing

Sample annotation

	1	2	3	4
A	CHO - WT - 1 - Live - NT.fcs CHO WT Live 1 NT	CHO - CCR5 - 1 - Live - NT.fcs CHO CCR5 Live 1 NT	HEK - WT - 1 - Live - NT.fcs HEK WT Live 1 NT	HEK - CCR5 - 1 - Live - NT.fcs HEK CCR5 Live 1 NT
B		CHO - CCR5 - 2 - Live - NT.fcs CHO CCR5 Live 2 NT	HEK - WT - 2 - Live - NT.fcs HEK WT Live 2 NT	HEK - CCR5 - 2 - Live - NT.fcs HEK CCR5 Live 2 NT
C	CHO - WT - 1 - Live - CCR5-Hek-1-85a.fcs CHO WT Live 1 aCCR5-Hek/1/85a	CHO - CCR5 - 1 - Live - CCR5-Hek-1-85a.fcs CHO CCR5 Live 1 aCCR5-Hek/1/85a	HEK - WT - 1 - Live - CCR5-Hek-1-85a.fcs HEK WT Live 1 aCCR5-Hek/1/85a	HEK - CCR5 - 1 - Live - CCR5-Hek-1-85a.fcs HEK CCR5 Live 1 aCCR5-Hek/1/85a
D		CHO - CCR5 - 2 - Live - CCR5-Hek-1-85a.fcs CHO CCR5 Live 2 aCCR5-Hek/1/85a	HEK - WT - 2 - Live - CCR5-Hek-1-85a.fcs HEK WT Live 2 aCCR5-Hek/1/85a	HEK - CCR5 - 2 - Live - CCR5-Hek-1-85a.fcs HEK CCR5 Live 2 aCCR5-Hek/1/85a
E	CHO - WT - 1 - Fixed+Tween - NT.fcs CHO WT Fixed+Tween 1 NT			HEK - CCR5 - 1 - Fixed+Tween - NT.fcs HEK CCR5 Fixed+Tween 1 NT
F	CHO - WT - 2 - Fixed+Tween - NT.fcs CHO WT Fixed+Tween 2 NT	CHO - CCR5 - 2 - Fixed+Tween - NT.fcs CHO CCR5 Fixed+Tween 2 NT		HEK - CCR5 - 2 - Fixed+Tween - NT.fcs HEK CCR5 Fixed+Tween 2 NT
G	CHO - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs CHO WT Fixed+Tween 1 aCCR5-Hek/1/85a	CHO - CCR5 - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs CHO CCR5 Fixed+Tween 1 aCCR5-Hek/1/85a	HEK - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs HEK WT Fixed+Tween 1 aCCR5-Hek/1/85a	HEK - CCR5 - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs HEK CCR5 Fixed+Tween 1 aCCR5-Hek/1/85a
H	CHO - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs CHO WT Fixed+Tween 2 aCCR5-Hek/1/85a	CHO - CCR5 - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs CHO CCR5 Fixed+Tween 2 aCCR5-Hek/1/85a		HEK - CCR5 - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs HEK CCR5 Fixed+Tween 2 aCCR5-Hek/1/85a

Data cleaning

Raw data

Raw data, FSC-A vs SSC-A

Outlier cleaning

Outlier cleaning, FSC-A vs SSC-A

Main cell population gating

FSC-A vs SSC-A, Main cell population gating

FSC-A vs SSC-A, Main cell population gated

Singlets cleaning, SSC

SSC-A vs SSC-H, SSC singlet gating

SSC-A vs SSC-H, SSC singlets gated

FSC-A vs SSC-A, SSC singlets gated

Singlets cleaning, FSC

FSC-A vs SSC-A, FSC singlet gating

FSC-A vs FSC-H, FSC singlet gating

FSC-A vs SSC-A, FSC singlet gated

Cleaned dataset

Cleaned dataset, FSC-A vs SSC-A

Cleaned dataset, Missing samples removed, FSC-A vs SSC-A

Data analysis

Data analysis, density plots

APC probe & cell mutation comparisons, APC-A

-1

Data analysis, bar graphs

APC probe & cell mutation comparisons, APC-A, Median fluorescence intensity

-1

Data analysis, interactive bar graphs

APC probe & cell mutation comparisons, APC-A, Median fluorescence intensity

-1

Data analysis, Data tables

Data table, Event analysis

Data table, individual replicates, long

Data table, individual replicates, wide

Data table, Statistics, long

Analysis parameters

Variable name	Variable description	Choice for the analysis
parameter_analysis_title	Name of your analysis	CCR5_CellScreen
parameter_channels_to_display	Channels to display	APC-A
parameter_comparisons_to_make_primary	Which parameters do you want to display the flow cytometry density plots on the same graphs (the other will be facets) (colors)	APC_probe
parameter_comparisons_to_make_secondary	Which parameters do you want to display the flow cytometry density plots on the same graphs (the other will be facets) (linetype)	cell_mutation
parameter_entity_of_interest	Which parameter do you want as the x axis of the bar graphs ?	sample
parameter_facets_to_remove	Which parameters do you want not to be included in the facets	template_name, sample
parameter_free_y	Type of scale for the density plots	free_y
parameter_gate_preset_fscsscs	Use a preset for the debris and main cloud gating on FSC and SSC ? (Will overide manually defined windows)	gate_preset_fscssc_cho
parameter_individual_trace_graphs	Data cleaning to perform	main_cell_pop_enabled, fsc_singlet_enabled, ssc_singlet_enabled
parameter_ncol_density_plots	Number of graphs in each columns for the density plots	3
parameter_output_graphs	Output non-interactive graphs ?	TRUE
parameter_process_from_script	Used to check if reporting was started from a script. Do not change.	FALSE
parameter_quantile_value_ceiling	Quantile ceiling for graphs	0.9999
parameter_quantile_value_floor	Quantile floor for graphs	0.01
parameter_radius_cloud	Multiplier for the radius of the main population selection (try 2.5 for PBMCs)	1.5
parameter_remove_empty	After gating, remove the samples that do not have an annotation in these categories	comments_1, placeholder
parameter_scale_density	Normalize the density plot maximum to 1?	FALSE
parameter_single_dataset_name	For batch processing. Do not modify	DrugDisc
parameter_theme_density_plots	Theme for the density plots ? (check https://ggplot2.tidyverse.org/reference/ggtheme.html for exemples)	theme_gray
parameter_window_debris	Approximate boundaries for the debris separated by semicolumns (SSC-A_floor;SSC-A_ceiling;FSC-A_floor;FSC-A_ceiling) (OPTIONAL)
parameter_window_of_interest	Approximate boundaries of the population of interest separated by semicolumns (SSC-A_floor;SSC-A_ceiling;FSC-A_floor;FSC-A_ceiling) (OPTIONAL)	0;1e60;1e6;1e15